The Sulawesi macaque species endemic to island of Sulawesi (Central Indonesia) have differentiated into seven morphologically distinct species in seven allopatric areas. The evolution of these species has been studied, however the evolutionary process and its genetic basis are still unclear. We determined exome sequences of seven species. The analyses of these data showed that the speciation of Sulawesi macaques has occurred in Sulawesi island just after the migration of common ancestral species of these macaques. Most of the SNPs were observed in one species (~90%) or shared between M. tonkeana and M. hecki, whereas a handful of SNPs were fixed differences. These fixed differences were located in ~100 genes including genes responsible for olfaction, and detoxification. These results demonstrate that the small number of genes with fixed differences may be responsible for local adaption and for preventing expansion of hybrid zones.